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Complete Genome Assembly of Staphylococcus epidermidis AmMS 205 K. W. Davenport,a H. E. Daligault,a T. D. Minogue,b K. A. Bishop-Lilly,c,d S. M. Broomall,e D. C. Bruce,a P. S. Chain,a S. R. Coyne,b K. G. Frey,c,d H. S. Gibbons,e J. Jaissle,b C. L. Redden,c,d C. N. Rosenzweig,e M. B. Scholz,a* H. Teshima, S. L. Johnsona Los Alamos National Laboratory (LANL), Los Alamos, New Mexico, USAa; Diagnostic Systems Division (DSD), United States Army Medical Research Institute of Infectious Diseases (USAMRIID), Fort Detrick, Maryland, USAb; Naval Medical Research Center (NMRC)-Frederick, Fort Detrick, Maryland, USAc; Henry M. Jackson Foundation, Bethesda, Maryland, USAd; United States Army Edgewood Chemical Biological Center (ECBC), Aberdeen Proving Ground, Maryland, USAe * Present address: M. B. Scholz, Michigan State University, East Lansing, Michigan, USA.
Received 8 September 2014 Accepted 30 September 2014 Published 6 November 2014 Citation Davenport KW, Daligault HE, Minogue TD, Bishop-Lilly KA, Broomall SM, Bruce DC, Chain PS, Coyne SR, Frey KG, Gibbons HS, Jaissle J, Redden CL, Rosenzweig CN, Scholz MB, Teshima H, Johnson SL. 2014. Complete genome assembly of Staphylococcus epidermidis AmMS 205. Genome Announc. 2(6):e01059-14. doi:10.1128/ genomeA.01059-14. Copyright © 2014 Davenport et al. This is an open-access article distributed under the terms of the Creative Commons Attribution 3.0 Unported license. Address correspondence to S. L. Johnson, [email protected].
S
taphylococcus epidermidis has been called an “accidental pathogen,” because it evolved to be a commensal rather than pathogenic microbe (1). Unlike Staphylococcus aureus, S. epidermidis produces only a small number of toxins and exoenzymes that cause tissue damage and its ability to act as an opportunistic pathogen depends on its ability to form biofilms that escape immune response (2). Despite the opportunistic nature of S. epidermidis infection, treatment costs in the United States alone are estimated at $2 billion annually (1). In this effort, we sequenced and assembled the genome of reference strain S. epidermidis AmMS 205 (ATCC 49134; CDC 73-57501). High-quality genomic DNA was extracted from a purified isolate using Qiagen Genome Tip-500 at USAMRIID-DSD. Specifically, a 100-mL bacterial culture was grown to the stationary phase and nucleic acid was extracted as per the manufacturer’s recommendations. Sequence data included both 100-bp Illumina standard data (307-fold genome coverage) and long-insert 454 paired-end data (8,237 ⫾ 2,059-bp insert, 29-fold genome coverage) (3, 4). The two datasets were assembled together in Newbler (Roche), and the consensus sequences were computationally shredded into 2-kbp overlapping fake reads (shreds). The raw reads were also assembled in Velvet, and those consensus sequences were computationally shredded into 1.5-kbp overlapping shreds (5). Draft data from all platforms were then assembled together with Allpaths, and the consensus sequences were computationally shredded into 10-kbp overlapping shreds (6). We then integrated the Newbler consensus shreds, Velvet consensus shreds, Allpaths consensus shreds, and a subset of the long-insert read-pairs using parallel Phrap (High Performance Software, LLC). Possible misassemblies were corrected and some gap closure was accomplished with manual editing in Consed (7–9). The complete genome assembly of S. epidermidis AmMS 205 includes a 2,500,626-bp circular chromosome (32.1% G⫹C content) and a 37,688-bp circular plasmid (27.3% G⫹C content) and
November/December 2014 Volume 2 Issue 6 e01059-14
was annotated using an Ergatis-based workflow (10) at LANL with minor manual curation. A total of 2,347 coding sequences (57 located on the plasmid) and 19 rRNA and 59 tRNA sequences were noted. At least 7 of the virulence factors noted by Otto (1) were found upon preliminary review of the annotation, all of which are located on the chromosome. Nucleotide sequence accession numbers. The chromosome (CP009046) and plasmid (CP009047) are publicly available in the NCBI database. ACKNOWLEDGMENTS Funding for this effort was provided by the Defense Threat Reduction Agency’s Joint Science and Technology Office (DTRA J9-CB/JSTO). This manuscript is approved by LANL for unlimited release (LA-UR-1426059). The views expressed in this article are those of the authors and do not necessarily reflect the official policy or position of the Department of the Navy, Department of Defense, or the U.S. Government.
REFERENCES 1. Otto M. 2009. Staphylococcus epidermidis—the “accidental” pathogen. Nat. Rev. Microbiol. 7:555–567. http://dx.doi.org/10.1038/nrmicro2182. 2. Vuong C, Otto M. 2002. Staphylococcus epidermidis infections. Microbes Infect. 4:481– 489. http://dx.doi.org/10.1016/S1286-4579(02)01563-0. 3. Bennett S. 2004. Solexa Ltd. Pharmacogenomics 5:433– 438. http:// dx.doi.org/10.1517/14622416.5.4.433. 4. Margulies M, Egholm M, Altman WE, Attiya S, Bader JS, Bemben LA, Berka J, Braverman MS, Chen Y-J, Chen Z, Dewell SB, Du L, Fierro JM, Gomes XV, Godwin BC, He W, Helgesen S, Ho CH, Irzyk GP, Jando SC, Alenquer MLI, Jarvie TP, Jirage KB, Kim J-B, Knight JR, Lanza JR, Leamon JH, Lefkowitz SM, Lei M, Li J, Lohman KL, Lu H, Makhijani VB, McDade KE, McKenna MP, Myers EW, Nickerson E, Nobile JR, Plant R, Puc BP, Ronan MT, Roth GT, Sarkis GJ, Simons JF, Simpson JW, Srinivasan M, Tartaro KR, Tomasz A, Vogt KA, Volkmer GA, Wang SH, Wang Y, Weiner MP, Yu P, Begley RF, Rothberg JM. 2005. Genome sequencing in microfabricated high-density picolitre reactors. Nature 437:376 –380. http://dx.doi.org/10.1038/nature03959. 5. Zerbino DR, Birney E. 2008. Velvet: algorithms for de novo short read
Genome Announcements
genomea.asm.org 1
Downloaded from http://genomea.asm.org/ on November 15, 2015 by guest
Staphylococcus epidermidis causes a large number of catheter-related sepsis infections annually in the United States. We present the 2.54-Mbp complete genome assembly of reference strain S. epidermidis AmMS 205, including a single 37.7-kbp plasmid. The annotated assembly is available in GenBank under accession numbers CP009046 and CP009047.
Davenport et al.
assembly using de Bruijn graphs. Genome Res. 18:821– 829. http:// dx.doi.org/10.1101/gr.074492.107. 6. Butler J, MacCallum I, Kleber M, Shlyakhter IA, Belmonte MK, Lander ES, Nusbaum C, Jaffe DB. 2008. ALLPATHS: de novo assembly of wholegenome shotgun microreads. Genome Res. 18:810 – 820. http:// dx.doi.org/10.1101/gr.7337908. 7. Ewing B, Hillier L, Wendl MC, Green P. 1998. Base-calling of automated sequencer traces using Phred. I: accuracy assessment. Genome Res. 8:175–185. http://dx.doi.org/10.1101/gr.8.3.175.
8. Ewing B, Green P. 1998. Base-calling of automated sequencer traces using Phred. II: error probabilities. Genome Res. 8:186 –194. 9. Gordon D, Abajian C, Green P. 1998. Consed: a graphical tool for sequence finishing. Genome Res. 8:195–202. http://dx.doi.org/10.1101/ gr.8.3.195. 10. Hemmerich C, Buechlein A, Podicheti R, Revanna KV, Dong Q. 2010. An Ergatis-based prokaryotic genome annotation Web server. Bioinformatics 26:1122–1124. http://dx.doi.org/10.1093/ bioinformatics/btq090.
Downloaded from http://genomea.asm.org/ on November 15, 2015 by guest
2 genomea.asm.org
Genome Announcements
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Complete Genome Assembly of Staphylococcus epidermidis AmMS 205 K. W. Davenport,a H. E. Daligault,a T. D. Minogue,b K. A. Bishop-Lilly,c,d S. M. Broomall,e D. C. Bruce,a P. S. Chain,a S. R. Coyne,b K. G. Frey,c,d H. S. Gibbons,e J. Jaissle,b C. L. Redden,c,d C. N. Rosenzweig,e M. B. Scholz,a* H. Teshima, S. L. Johnsona Los Alamos National Laboratory (LANL), Los Alamos, New Mexico, USAa; Diagnostic Systems Division (DSD), United States Army Medical Research Institute of Infectious Diseases (USAMRIID), Fort Detrick, Maryland, USAb; Naval Medical Research Center (NMRC)-Frederick, Fort Detrick, Maryland, USAc; Henry M. Jackson Foundation, Bethesda, Maryland, USAd; United States Army Edgewood Chemical Biological Center (ECBC), Aberdeen Proving Ground, Maryland, USAe * Present address: M. B. Scholz, Michigan State University, East Lansing, Michigan, USA.
Received 8 September 2014 Accepted 30 September 2014 Published 6 November 2014 Citation Davenport KW, Daligault HE, Minogue TD, Bishop-Lilly KA, Broomall SM, Bruce DC, Chain PS, Coyne SR, Frey KG, Gibbons HS, Jaissle J, Redden CL, Rosenzweig CN, Scholz MB, Teshima H, Johnson SL. 2014. Complete genome assembly of Staphylococcus epidermidis AmMS 205. Genome Announc. 2(6):e01059-14. doi:10.1128/ genomeA.01059-14. Copyright © 2014 Davenport et al. This is an open-access article distributed under the terms of the Creative Commons Attribution 3.0 Unported license. Address correspondence to S. L. Johnson, [email protected].
S
taphylococcus epidermidis has been called an “accidental pathogen,” because it evolved to be a commensal rather than pathogenic microbe (1). Unlike Staphylococcus aureus, S. epidermidis produces only a small number of toxins and exoenzymes that cause tissue damage and its ability to act as an opportunistic pathogen depends on its ability to form biofilms that escape immune response (2). Despite the opportunistic nature of S. epidermidis infection, treatment costs in the United States alone are estimated at $2 billion annually (1). In this effort, we sequenced and assembled the genome of reference strain S. epidermidis AmMS 205 (ATCC 49134; CDC 73-57501). High-quality genomic DNA was extracted from a purified isolate using Qiagen Genome Tip-500 at USAMRIID-DSD. Specifically, a 100-mL bacterial culture was grown to the stationary phase and nucleic acid was extracted as per the manufacturer’s recommendations. Sequence data included both 100-bp Illumina standard data (307-fold genome coverage) and long-insert 454 paired-end data (8,237 ⫾ 2,059-bp insert, 29-fold genome coverage) (3, 4). The two datasets were assembled together in Newbler (Roche), and the consensus sequences were computationally shredded into 2-kbp overlapping fake reads (shreds). The raw reads were also assembled in Velvet, and those consensus sequences were computationally shredded into 1.5-kbp overlapping shreds (5). Draft data from all platforms were then assembled together with Allpaths, and the consensus sequences were computationally shredded into 10-kbp overlapping shreds (6). We then integrated the Newbler consensus shreds, Velvet consensus shreds, Allpaths consensus shreds, and a subset of the long-insert read-pairs using parallel Phrap (High Performance Software, LLC). Possible misassemblies were corrected and some gap closure was accomplished with manual editing in Consed (7–9). The complete genome assembly of S. epidermidis AmMS 205 includes a 2,500,626-bp circular chromosome (32.1% G⫹C content) and a 37,688-bp circular plasmid (27.3% G⫹C content) and
November/December 2014 Volume 2 Issue 6 e01059-14
was annotated using an Ergatis-based workflow (10) at LANL with minor manual curation. A total of 2,347 coding sequences (57 located on the plasmid) and 19 rRNA and 59 tRNA sequences were noted. At least 7 of the virulence factors noted by Otto (1) were found upon preliminary review of the annotation, all of which are located on the chromosome. Nucleotide sequence accession numbers. The chromosome (CP009046) and plasmid (CP009047) are publicly available in the NCBI database. ACKNOWLEDGMENTS Funding for this effort was provided by the Defense Threat Reduction Agency’s Joint Science and Technology Office (DTRA J9-CB/JSTO). This manuscript is approved by LANL for unlimited release (LA-UR-1426059). The views expressed in this article are those of the authors and do not necessarily reflect the official policy or position of the Department of the Navy, Department of Defense, or the U.S. Government.
REFERENCES 1. Otto M. 2009. Staphylococcus epidermidis—the “accidental” pathogen. Nat. Rev. Microbiol. 7:555–567. http://dx.doi.org/10.1038/nrmicro2182. 2. Vuong C, Otto M. 2002. Staphylococcus epidermidis infections. Microbes Infect. 4:481– 489. http://dx.doi.org/10.1016/S1286-4579(02)01563-0. 3. Bennett S. 2004. Solexa Ltd. Pharmacogenomics 5:433– 438. http:// dx.doi.org/10.1517/14622416.5.4.433. 4. Margulies M, Egholm M, Altman WE, Attiya S, Bader JS, Bemben LA, Berka J, Braverman MS, Chen Y-J, Chen Z, Dewell SB, Du L, Fierro JM, Gomes XV, Godwin BC, He W, Helgesen S, Ho CH, Irzyk GP, Jando SC, Alenquer MLI, Jarvie TP, Jirage KB, Kim J-B, Knight JR, Lanza JR, Leamon JH, Lefkowitz SM, Lei M, Li J, Lohman KL, Lu H, Makhijani VB, McDade KE, McKenna MP, Myers EW, Nickerson E, Nobile JR, Plant R, Puc BP, Ronan MT, Roth GT, Sarkis GJ, Simons JF, Simpson JW, Srinivasan M, Tartaro KR, Tomasz A, Vogt KA, Volkmer GA, Wang SH, Wang Y, Weiner MP, Yu P, Begley RF, Rothberg JM. 2005. Genome sequencing in microfabricated high-density picolitre reactors. Nature 437:376 –380. http://dx.doi.org/10.1038/nature03959. 5. Zerbino DR, Birney E. 2008. Velvet: algorithms for de novo short read
Genome Announcements
genomea.asm.org 1
Downloaded from http://genomea.asm.org/ on November 15, 2015 by guest
Staphylococcus epidermidis causes a large number of catheter-related sepsis infections annually in the United States. We present the 2.54-Mbp complete genome assembly of reference strain S. epidermidis AmMS 205, including a single 37.7-kbp plasmid. The annotated assembly is available in GenBank under accession numbers CP009046 and CP009047.
Davenport et al.
assembly using de Bruijn graphs. Genome Res. 18:821– 829. http:// dx.doi.org/10.1101/gr.074492.107. 6. Butler J, MacCallum I, Kleber M, Shlyakhter IA, Belmonte MK, Lander ES, Nusbaum C, Jaffe DB. 2008. ALLPATHS: de novo assembly of wholegenome shotgun microreads. Genome Res. 18:810 – 820. http:// dx.doi.org/10.1101/gr.7337908. 7. Ewing B, Hillier L, Wendl MC, Green P. 1998. Base-calling of automated sequencer traces using Phred. I: accuracy assessment. Genome Res. 8:175–185. http://dx.doi.org/10.1101/gr.8.3.175.
8. Ewing B, Green P. 1998. Base-calling of automated sequencer traces using Phred. II: error probabilities. Genome Res. 8:186 –194. 9. Gordon D, Abajian C, Green P. 1998. Consed: a graphical tool for sequence finishing. Genome Res. 8:195–202. http://dx.doi.org/10.1101/ gr.8.3.195. 10. Hemmerich C, Buechlein A, Podicheti R, Revanna KV, Dong Q. 2010. An Ergatis-based prokaryotic genome annotation Web server. Bioinformatics 26:1122–1124. http://dx.doi.org/10.1093/ bioinformatics/btq090.
Downloaded from http://genomea.asm.org/ on November 15, 2015 by guest
2 genomea.asm.org
Genome Announcements
November/December 2014 Volume 2 Issue 6 e01059-14
